MBL leads effort to update E. coli genome

Project aims to consolidate information, coordinate efforts

E.coli is one of the most important model organisms for molecular science today and is arguably the single organism about which the most is known. The genes of higher-level plants and animals, even humans, are often understood by their similarity to E. coli genes. As such, the accuracy and completeness of E.coli genome information is of great importance to the scientific community.

In an attempt to consolidate the efforts of scientists working independently on the genome of the E.coli K-12 strain, an international team of biologists, led by MBL (Marine Biological Laboratory) scientists Monica Riley and Margrethe “Gretta” Serres, has published a comprehensive, updated description of all 4,500 E. coli K-12 genes. The data is presented in the January 5, 2006 online issue of the journal Nucleic Acids Research.

“The E. coli scientific community is scattered,” said Riley, a senior scientist in the MBL’s Josephine Bay Paul Center for Comparative Molecular Biology and Evolution. “We determined that we needed to get together and pool everything we know into one package. E. coli is one of the most important model organisms for molecular science today. Our work will help move this forward.”

A group of 19 scientists from four countries updated the annotation of E. coli K-12 at two MBL workshops organized by Riley and Serres. Annotation involves identification of genes, and their starting and ending sites, as well as the description of gene products. The process helps scientists to determine gene function.

During the MBL workshops, Riley and her colleagues assigned known or predicted gene functions to each E. coli K-12 product based on previously known experimental evidence or sequence analysis. “We cooperated to an amazing extent, reviewing every single one of 4,500 genes of E. coli K-12,” said Riley. The scientists developed the best consensus on the status and properties of each of the E.coli K-12 genes at the present moment. Their goal was not to create a new database, but to present a comprehensive, updated annotation of E.coli K-12, which would be readily available to the public. “Our work puts a searchlight on the fraction of E. coli genes that are unknown and will accelerate laboratory work on the unknown functions with the goal of knowing what every gene does in the living organism,” said Riley.

According to Riley, currently there is no funding by an agency for any kind of coordinated E. coli annotation effort, however interested members of the E. coli community are applying to NIH for support to establish a K-12 information resource. “Interaction among the scientists accelerates discovery and the hope is that this kind of work will soon be centralized,” she said. “This would provide more efficient coordination of scientific groups that are working independently.”